Search Packages

cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

libbiosmoother

On-the-fly processing and visualization of interactome data.

hicstuff

Simple library/pipeline to generate and handle Hi-C data.

clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

hic2cool

Lightweight converter between hic and cool contact matrices.

gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

pypairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

mustache-hic

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

hiclift

Convert genomic coordinates of contact pairs from one assembly to another.

metator

Metagenomic binning based on Hi-C data

coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

neoloop

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

runhic

An easy-to-use Hi-C data processing software supporting distributed computation.

instagraal

Large genome reassembly based on Hi-C data, continuation of GRAAL

trackc

trackc aims to produce beautiful genome tracks that are highly customizable

pareidolia

Multi-sample change detection in Hi-C patterns

hicpeaks

A Python implementation for BH-FDR and HiCCUPS

diffdomain-py3

DiffDomain is a statistically sound method for detecting differential TADs between conditions

biosmoother

On-the-fly processing and visualization of interactome data

chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices